Cobalt in PDB 2gru: Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+

The structure of Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+, PDB code: 2gru was solved by E.Nango, T.Kumasaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.72 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.569, 70.108, 81.569, 90.00, 117.61, 90.00
R / Rfree (%)	17.4 / 22.3

The binding sites of Cobalt atom in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+ (pdb code 2gru). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+, PDB code: 2gru:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Co601 b:14.4 occ:1.00 OE1 A:GLU183 2.0 11.0 1.0 OBI A:EXO607 2.1 20.4 1.0 NE2 A:HIS262 2.1 13.8 1.0 NE2 A:HIS246 2.2 16.2 1.0 OBG A:EXO607 2.3 29.4 1.0 O A:HOH695 2.3 24.4 1.0 CD2 A:HIS262 2.9 15.1 1.0 CBB A:EXO607 3.0 29.7 1.0 CD A:GLU183 3.0 10.6 1.0 CBA A:EXO607 3.0 30.6 1.0 CE1 A:HIS246 3.1 16.7 1.0 CD2 A:HIS246 3.2 17.3 1.0 CE1 A:HIS262 3.3 14.6 1.0 OE2 A:GLU183 3.4 7.8 1.0 OD2 A:ASP135 3.9 19.5 1.0 CG A:HIS262 4.2 15.4 1.0 ND1 A:HIS246 4.2 16.9 1.0 ND1 A:HIS262 4.3 15.9 1.0 CG A:GLU183 4.3 11.5 1.0 CG A:HIS246 4.3 17.7 1.0 CG1 A:ILE266 4.4 15.7 1.0 O A:HOH728 4.4 20.6 1.0 CBC A:EXO607 4.4 31.1 1.0 CBF A:EXO607 4.4 35.4 1.0 NZ A:LYS186 4.5 10.8 1.0 O A:HOH754 4.8 38.7 1.0 CD1 A:ILE266 4.8 13.3 1.0 OBJ A:EXO607 4.8 33.1 1.0 CBH A:EXO607 4.9 38.2 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co602 b:14.4 occ:1.00 OE1 B:GLU183 2.0 12.9 1.0 NE2 B:HIS262 2.1 9.9 1.0 OAH B:CAK609 2.1 21.3 1.0 NE2 B:HIS246 2.2 14.0 1.0 OAG B:CAK609 2.3 19.5 1.0 O B:HOH701 2.6 24.8 1.0 CD2 B:HIS262 2.9 11.6 1.0 CD B:GLU183 3.0 11.3 1.0 CE1 B:HIS246 3.0 17.4 1.0 CAB B:CAK609 3.1 28.2 1.0 CE1 B:HIS262 3.1 12.4 1.0 CAA B:CAK609 3.1 29.3 1.0 CD2 B:HIS246 3.3 13.6 1.0 OE2 B:GLU183 3.4 9.8 1.0 OD2 B:ASP135 3.9 13.3 1.0 O B:HOH635 4.1 33.3 1.0 CG B:HIS262 4.1 14.5 1.0 ND1 B:HIS262 4.2 16.5 1.0 ND1 B:HIS246 4.2 13.0 1.0 CG B:GLU183 4.2 9.9 1.0 CG1 B:ILE266 4.3 19.2 1.0 CG B:HIS246 4.3 13.7 1.0 CAC B:CAK609 4.4 30.0 1.0 O B:HOH745 4.5 43.3 1.0 CAF B:CAK609 4.5 33.7 1.0 NZ B:LYS186 4.6 10.9 1.0 CD1 B:ILE266 4.7 17.1 1.0 OAI B:CAK609 4.9 32.3 1.0

E.Nango, T.Kumasaka, T.Hirayama, N.Tanaka, T.Eguchi. Structure of 2-Deoxy-Scyllo-Inosose Synthase, A Key Enzyme in the Biosynthesis of 2-Deoxystreptamine-Containing Aminoglycoside Antibiotics, in Complex with A Mechanism-Based Inhibitor and Nad+ Proteins V. 70 517 2008.
ISSN: ISSN 0887-3585
PubMed: 17879343
DOI: 10.1002/PROT.21526